Tuyển tập các báo cáo nghiên cứu về sinh học được đăng trên tạp chí y học Molecular Biology cung cấp cho các bạn kiến thức về ngành sinh học đề tài: Accuracy of phylogeny reconstruction methods combining overlapping gene data sets. | Kupczok et al. Algorithms for Molecular Biology 2010 5 37 http content 5 1 37 AMR ALGORITHMS FOR MOLECULAR BIOLOGY RESEARCH Open Access Accuracy of phylogeny reconstruction methods combining overlapping gene data sets Anne Kupczok1 2 Heiko A Schmidt1 Arndt von Haeseler1 Abstract Background The availability of many gene alignments with overlapping taxon sets raises the question of which strategy is the best to infer species phylogenies from multiple gene information. Methods and programs abound that use the gene alignment in different ways to reconstruct the species tree. In particular different methods combine the original data at different points along the way from the underlying sequences to the final tree. Accordingly they are classified into superalignment supertree and medium-level approaches. Here we present a simulation study to compare different methods from each of these three approaches. Results We observe that superalignment methods usually outperform the other approaches over a wide range of parameters including sparse data and gene-specific evolutionary parameters. In the presence of high incongruency among gene trees however other combination methods show better performance than the superalignment approach. Surprisingly some supertree and medium-level methods exhibit on average worse results than a single gene phylogeny with complete taxon information. Conclusions For some methods using the reconstructed gene tree as an estimation of the species tree is superior to the combination of incomplete information. Superalignment usually performs best since it is less susceptible to stochastic error. Supertree methods can outperform superalignment in the presence of gene-tree conflict. Background The phylogenetic information inherent in sequence data from different genes can be combined to yield a species phylogeny rather than gene trees. The gene data for these phylogenies are mainly collected following two strategies a using only genes that .
